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A New Method for Constructing High-Resolution Phylogenomic Topologies Using Core Gene-Associated MNP Markers: A Case Study From Agaricus bisporus

Summary

Scientists developed a new method to accurately identify and distinguish different strains of button mushrooms using genetic markers derived from core genes. This method is more accurate and simpler than previous approaches and can be applied to other mushroom species and fungi. The research helps mushroom farmers and breeders properly identify cultivars and protect their varieties from unauthorized propagation.

Background

Accurate strain identification is essential for economically significant fungi to understand their agronomic traits and pathogenicity. Traditional identification methods face challenges with limited accuracy, high workloads, and reproducibility issues. Multiple nucleotide polymorphism (MNP) markers have recently improved accuracy but remain complex and lack cross-species utility.

Objective

This study develops a novel method for constructing high-resolution phylogenomic topologies using core gene-associated MNP (cgMNP) markers for Agaricus bisporus. The research aims to create strain-level discrimination tools with improved transferability across fungal species while maintaining high accuracy and reproducibility.

Results

All strains were precisely identified using cgMNP sequences and genetic distance analysis. cgMNP markers demonstrated superior congruence with whole-genome SNP data compared to UFCG markers. The markers successfully transferred to additional fungal species, with high coverage across 2095 representative fungal genome assemblies, demonstrating cross-species applicability.

Conclusion

Core gene-associated MNP markers provide a robust and reliable method for strain-level discrimination in fungi with high resolution and strong congruence with whole-genome data. The success of this approach in A. bisporus sets a promising precedent for broader application across fungal taxa, advancing phylogenomic analysis and strain identification.
  • Published in:Microbial Biotechnology,
  • Study Type:Methodological Research Study,
  • Source: 10.1111/1751-7915.70070, PMID: 39976373
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